Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

Abstract

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breedspecific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, .90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index C for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.

Rethinking dog domestication by integrating genetics, archeology, and biogeography

“…Bernese Mountain Dogs (18) and Italian Greyhounds (22) vanished completely and many other breeds suffered significant bottlenecks (Table S1). Bolstering or recreating these breeds was accomplished by crossing numerous other breeds, a practice that obscured whatever genetic signatures of their early heritage that existed before the World Wars, and ultimately led to highly inbred modern populations (23). Interestingly, the recent genetic homogenization has occurred despite the increase in phenotypic disparity as breeders have simultaneously closed breeding lines and selected for extreme morphological traits (24).…”

A pedigree-based analysis of mitochondrial DNA diversity in a dog population on the example of German Hovawarts

“…Secondly, usually only one bitch from a litter is included in breeding (the average in German Hovawarts is 1.15). The one-litter kennels observed in many dog breeds (Leroy et al, 2007;Calboli et al, 2008;Mäki, 2010), which produce disproportionately low numbers of breeding bitches , could also play a role in the random loss of mtDNA haplotypes present in a population. A general rule of "one kennel-one breeding bitch" also facilitates the extinction of dam lines.…”

Evaluation of the effectiveness of introducing new alleles into the gene pool of a rare dog breed: Polish Hound as the example

“…Mäki (2010), in her study on two breeds (Nova Scotia Retriever, Lancashire Heeler), proposed crosses with other breeds (NS) or with unregistered farm dogs (LS) to increase the genetic diversity of the breeds. Calboli et al (2008) suggested relaxing breed rules to permit controlled outcrossing. Unfortunately, the case of the Polish Hounds indicates basic problems with such improvement programmes.…”

“…These analyses have indicated a number of unfavourable occurrences in dog breeding, such as a high level of inbreeding, high disproportion in the breeding use of sires, a low number of breed founders and strong imbalance in their contributions to a gene pool, all of which might result in the negative effects observed in the deteriorating health condition of a given breed and negatively influence its long-term perspectives. One way of enriching a limited gene pool is to introduce dogs of other breeds or of unknown origin that are phenotypically similar to a given breed (Leroy et al, 2006;Calboli et al, 2008;Mäki, 2010). However, the effectiveness of introducing new alleles into the gene pool of the breed depends mainly on breeders' will to use such dogs in breeding.…”